Ejemplo n.º 1
0
def getChipDisplayedNameSecondaryPrefix(chipDisplayedName):
    """
    Returns all the second portion of the chip displayed name for UI to display
    e.g., for chip name "318 Select", return "Select"
    """
    isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)

    return prefixes[-1] if len(prefixes) > 1 else ""
Ejemplo n.º 2
0
def getChipDisplayedNamePrimaryPrefix(chipDisplayedName):
    """
    Returns all the primary chip displayed name for UI to display
    e.g., for chip name "318 Select", return 318
    """
    isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)

    return prefixes[0]
Ejemplo n.º 3
0
def getChipDisplayedNameSecondaryPrefix(chipDisplayedName):
    """
    Returns all the second portion of the chip displayed name for UI to display
    e.g., for chip name "318 Select", return "Select"
    """
    isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)

    return prefixes[-1] if len(prefixes) > 1 else ""
Ejemplo n.º 4
0
def getChipDisplayedNamePrimaryPrefix(chipDisplayedName):
    """
    Returns all the primary chip displayed name for UI to display
    e.g., for chip name "318 Select", return 318
    """
    isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)

    return prefixes[0]
Ejemplo n.º 5
0
    def __init__(self, sh_type):
        super(KitsStepData, self).__init__(sh_type)
        self.resourcePath = "rundb/plan/page_plan/page_plan_kits.html"
        self.prev_step_url = reverse("page_plan_application")
        self.next_step_url = reverse("page_plan_plugins")

        # 20130827-test
        # self._dependsOn.append(StepNames.IONREPORTER)

        self._dependsOn.append(StepNames.APPLICATION)
        self._dependsOn.append(StepNames.BARCODE_BY_SAMPLE)

        self.savedFields[KitsFieldNames.SAMPLE_PREPARATION_KIT] = None
        self.prepopulatedFields[
            KitsFieldNames.SAMPLE_PREP_KITS] = KitInfo.objects.filter(
                kitType="SamplePrepKit", isActive=True).order_by("description")

        self.savedFields[KitsFieldNames.LIBRARY_KIT_NAME] = None
        self.prepopulatedFields[
            KitsFieldNames.LIB_KITS] = KitInfo.objects.filter(
                kitType__in=["LibraryKit", "LibraryPrepKit"],
                isActive=True).order_by("description")

        self.savedFields[KitsFieldNames.LIBRARY_KEY] = None
        self.prepopulatedFields[
            KitsFieldNames.FORWARD_LIB_KEYS] = LibraryKey.objects.filter(
                direction="Forward",
                runMode="single").order_by("-isDefault", "name")
        self.savedFields[KitsFieldNames.LIBRARY_KEY] = self.prepopulatedFields[
            KitsFieldNames.FORWARD_LIB_KEYS][0].sequence

        self.savedFields[KitsFieldNames.TF_KEY] = GlobalConfig.get(
        ).default_test_fragment_key

        self.savedFields[KitsFieldNames.FORWARD_3_PRIME_ADAPTER] = None
        self.prepopulatedFields[
            KitsFieldNames.
            FORWARD_3_ADAPTERS] = ThreePrimeadapter.objects.filter(
                direction="Forward",
                runMode="single").order_by("-isDefault", "chemistryType",
                                           "name")
        self.savedFields[
            KitsFieldNames.FORWARD_3_PRIME_ADAPTER] = self.prepopulatedFields[
                KitsFieldNames.FORWARD_3_ADAPTERS][0].sequence

        self.savedFields[KitsFieldNames.FLOW_ORDER] = None
        self.prepopulatedFields[
            KitsFieldNames.FLOW_ORDERS] = FlowOrder.objects.filter(
                isActive=True).order_by("-isDefault", "description")
        self.savedFields[KitsFieldNames.FLOW_ORDER] = None

        self.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME] = None
        # no longer default to OneTouch
        # self.savedFields[KitsFieldNames.TEMPLATE_KIT_TYPE] = KitsFieldNames.ONE_TOUCH
        self.savedFields[KitsFieldNames.TEMPLATE_KIT_TYPE] = None

        oneTouchDict = {
            KitsFieldNames.KIT_VALUES:
            KitInfo.objects.filter(
                kitType__in=["TemplatingKit", "AvalancheTemplateKit"],
                isActive=True).exclude(
                    samplePrep_instrumentType="IA").order_by("description"),
            KitsFieldNames.APPLICATION_DEFAULT:
            None,
        }

        isoAmpDict = {
            KitsFieldNames.KIT_VALUES:
            KitInfo.objects.filter(
                kitType__in=["TemplatingKit"],
                isActive=True,
                samplePrep_instrumentType="IA",
            ).order_by("description"),
            KitsFieldNames.APPLICATION_DEFAULT:
            None,
        }
        ionChefDict = {
            KitsFieldNames.KIT_VALUES:
            KitInfo.objects.filter(kitType="IonChefPrepKit",
                                   isActive=True).order_by("description"),
            KitsFieldNames.APPLICATION_DEFAULT:
            None,
        }

        self.prepopulatedFields[
            KitsFieldNames.TEMPLATE_KIT_TYPES] = OrderedDict([
                (KitsFieldNames.ONE_TOUCH, oneTouchDict),
                (KitsFieldNames.ION_CHEF, ionChefDict),
                (KitsFieldNames.ISO_AMP, isoAmpDict),
            ])
        self.ModelsSamplePrepInstrumentToLabelsSamplePrepInstrumentAsDict = {
            KitsFieldNames.ONE_TOUCH: SamplePrepInstrument.OT,
            KitsFieldNames.ION_CHEF: SamplePrepInstrument.IC,
            KitsFieldNames.ISO_AMP: SamplePrepInstrument.IA,
        }

        self.savedFields[KitsFieldNames.SEQUENCE_KIT_NAME] = None
        self.prepopulatedFields[
            KitsFieldNames.SEQ_KITS] = KitInfo.objects.filter(
                kitType="SequencingKit", isActive=True).order_by("description")

        self.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME] = None
        self.prepopulatedFields[
            KitsFieldNames.TEMPLATE_KITS] = KitInfo.objects.filter(
                kitType__in=[
                    "TemplatingKit", "AvalancheTemplateKit", "IonChefPrepKit"
                ],
                isActive=True,
            ).order_by("description")

        self.savedFields[KitsFieldNames.CONTROL_SEQUENCE] = None
        self.prepopulatedFields[
            KitsFieldNames.CONTROL_SEQ_KITS] = KitInfo.objects.filter(
                kitType="ControlSequenceKit",
                isActive=True).order_by("description")

        self.savedFields[KitsFieldNames.CHIP_TYPE] = None
        self.prepopulatedFields[
            KitsFieldNames.
            INSTRUMENT_TYPES] = Chip.getInstrumentTypesForActiveChips(
                include_undefined=False)
        self.prepopulatedFields[KitsFieldNames.CHIP_TYPES] = list(
            Chip.objects.filter(isActive=True).order_by(
                "description", "name").distinct("description"))

        self.savedFields[KitsFieldNames.BARCODE_ID] = None
        self.prepopulatedFields[KitsFieldNames.BARCODES] = list(
            dnaBarcode.objects.filter(
                active=True).values("name").distinct().order_by("name"))

        gc = GlobalConfig.get()
        self.savedFields[
            KitsFieldNames.IS_DUPLICATED_READS] = gc.mark_duplicates

        self.savedFields[
            KitsFieldNames.BASE_RECALIBRATE] = gc.base_recalibration_mode

        self.prepopulatedFields[
            KitsFieldNames.BASE_RECALIBRATION_MODES] = OrderedDict()
        self.prepopulatedFields[
            KitsFieldNames.BASE_RECALIBRATION_MODES]["standard_recal"] = {
                "text":
                _("workflow.step.kits.base_recalibration_modes.standard_recal"
                  ),
                "title":
                _("workflow.step.kits.base_recalibration_modes.standard_recal.title"
                  ),
            }  # "Default Calibration"
        self.prepopulatedFields[
            KitsFieldNames.BASE_RECALIBRATION_MODES]["panel_recal"] = {
                "text":
                _("workflow.step.kits.base_recalibration_modes.panel_recal"),
                "title":
                _("workflow.step.kits.base_recalibration_modes.panel_recal.title"
                  ),
            }  # "Enable Calibration Standard"
        self.prepopulatedFields[
            KitsFieldNames.BASE_RECALIBRATION_MODES]["blind_recal"] = {
                "text":
                _("workflow.step.kits.base_recalibration_modes.blind_recal"),
                "title":
                _("workflow.step.kits.base_recalibration_modes.blind_recal.title"
                  ),
            }  # "Blind Calibration"
        self.prepopulatedFields[
            KitsFieldNames.BASE_RECALIBRATION_MODES]["no_recal"] = {
                "text":
                _("workflow.step.kits.base_recalibration_modes.no_recal"),
                "title":
                _("workflow.step.kits.base_recalibration_modes.no_recal.title"
                  ),
            }  # "No Calibration"

        self.savedFields[KitsFieldNames.REALIGN] = gc.realign

        self.savedFields[KitsFieldNames.FLOWS] = 0
        self.savedFields[KitsFieldNames.LIBRARY_READ_LENGTH] = 0
        self.savedFields[KitsFieldNames.READ_LENGTH] = 0

        self.prepopulatedFields[
            KitsFieldNames.IS_BARCODE_KIT_SELECTION_REQUIRED] = False

        self.prepopulatedFields[KitsFieldNames.TEMPLATING_SIZE_CHOICES] = [
            "200", "400"
        ]
        self.savedFields[KitsFieldNames.TEMPLATING_SIZE] = ""
        # For raptor templating kits, templating size cannot be used to drive UI behavior or db persistence.  Use read length instead.
        self.prepopulatedFields[KitsFieldNames.READ_LENGTH_CHOICES] = [
            "200", "400"
        ]
        self.prepopulatedFields[
            KitsFieldNames.FLOWS_FROM_CATEGORY_RULES] = json.dumps(
                KitInfo._category_flowCount_rules)

        self.savedFields[KitsFieldNames.SAMPLE_PREP_PROTOCOL] = None
        self.prepopulatedFields[
            KitsFieldNames.SAMPLE_PREP_PROTOCOLS] = common_CV.objects.filter(
                isActive=True, cv_type="samplePrepProtocol").order_by("uid")
        self.prepopulatedFields[KitsFieldNames.PLAN_CATEGORIES] = ""
        self.savedFields[KitsFieldNames.ADVANCED_SETTINGS_CHOICE] = "default"
        self.prepopulatedFields[KitsFieldNames.ADVANCED_SETTINGS] = "{}"

        self.sh_type = sh_type